Assessment of the Effects of Environmental Perturbations on Soil Ecology in A Terrestrial Mesocosm

Abstract

AbstractClimate change is altering ecosystems in unprecedented ways and necessitates the development of strategies that model ecosystems and allow for the evaluation of environmental impacts of perturbations: including climate events, novel approaches to agronomy or ecosystem management, and impacts of bio-industry and biotechnology innovations. Mesocosms present a platform to model some of the complexity of an ecosystem, while still being controlled and reproducible enough that they can be used to ask targeted questions and systematically assess the impacts of perturbation events. Herein, we established a methodological pipeline to assess the impact of three perturbation events (hydration, nutrification, contamination) upon plant-associated microbial communities using a terrestrial mesocosm. Mesocosms were assessed over a 30-day time-course following environmental perturbations, including modeling contamination with a foreign microbe via the introduction ofSaccharomyces cerevisiae. We developed and applied a suite of diagnostic and bioinformatic analyses, including digital droplet PCR, microscopy, and phylogenomic analyses to assess the impacts of a perturbation event in a system that models a terrestrial ecosystem. The resultant data show that our mesocosms are dynamic yet reproducible, and that the analysis pipeline presented here allowed for a longitudinal assessment of microbial population dynamics and abiotic soil characteristics following perturbations, as well as the fate of yeast in the soil. Notably, our data indicate that a single perturbation event can have long-lasting impact upon soil composition and underlying microbial populations. Thus, this approach can be used to ask targeted questions as well as gain insights on broader ecological trends of soil perturbation events.ImportanceSoils are key to a healthy environment, but the impact of human activities and climate change upon soil microbiomes remains unclear. It is challenging to model the complexity of an ecosystem in a laboratory; however, to gain insight on how ecosystems are impacted by outside perturbations it is valuable to develop approaches that mimic an environmental system. Here, we developed a mesocosm that uses readily accessible components that come together to model a terrestrial ecosystem which is coupled with an analysis pipeline to assess how various perturbations impact the soil. We demonstrate the utility of this approach by tracking the effects of three perturbations (water, nutrition, contamination with yeast) on the soil over the course of 30 days. Our results demonstrate that these treatments can have lasting impacts on the soil. These findings and the methods presented here could be useful to other researchers assessing how ecosystems respond to perturbations.HighlightsWe developed a pipeline using terrestrial mesocosms that allow for the analysis of how perturbations impact soil systems and demonstrate that it is effective for targeted detection of a microbe of interest as well as global phylogenomic observation of ecological changes due to external perturbation events.digital droplet PCR was adapted to track a low abundance, non-native microbe in soil mesocosms.Temporal sampling allowed for the longitudinal observation of soil response to a one-time perturbance.Introduction of yeast and its associated growth media conferred an expansion of total biomass and increase in alpha-diversity and shifts in the beta-diversity of the soil microbiome.Treatment with media or yeast resulted in the expansion in the relative contribution of fungal biomass and an increase in the relative abundances ofSaccharomycetes and Trellomycetes,with decreases inSordariomycetes, Leotiomycetes, and EurotomycetesMedia or yeastintroductionalso resulted in an expansion of the relative abundances ofGammaproteobacteria, Bacilli,andBacteroidia,and decreases inActinomycetiaandAcidobacteria.